Table 2. SNP markers, genes affected by the SNPs, and primers.
| SNP | SCHU S4a SNP position | SCHU S4 locus ID | SCHU S4 gene | SNP state | Primerb | Primer sequencesc |
| F.1 | 1312210, | FTTr04, | 16S | T | D | gcgggcCTATGGATCGTAGCCTTGGt |
| 1379332, | FTTr10, | Gd | A | gcgggcagggcggcCTATGGATCGTAGCCTTGGg | ||
| 1772676 | FTTr07 | C | AGTTGGAAACGACTGTTAATACCGCA | |||
| T/N.1 | 83976 | FTT0080 | tpiA | A | D | gcgggcAGAAACACATCAATTTATTCGTTCa |
| G | A | gcgggcagggcggcAGAAACACATCAATTTATTCGTTCg | ||||
| C | AGCATTTTCAGCTTTTAGGCTACCA | |||||
| T.1 | 1165690 | FTT1150c | putA | C | D | gcgggcagggcggcTGTTGAAAAAGCTCATATGTCAAGc |
| T | A | gcgggcTGTTGAAAAAGCTCATATGTCAAGt | ||||
| C | TCATACTCGATCATAAACGCATCA | |||||
| N.1 | 83943 | FTT0080 | tpiA | T | D | gcgggcACAGGAGTTGTGGCTTCACTAGAt |
| G | A | gcgggcagggcggcACAGGAGTTGTGGCTTCACTAGAg | ||||
| C | CATCAACTTTAGCTAACAATGAACGAAT | |||||
| N.2 | 910194 | FTT0901 | lpnA | A | D | gcgggcTGTAATCTTACACTTCCTTGTGGa |
| G | A | gcgggcagggcggcTGTAATCTTACACTTCCTTGTGGg | ||||
| C | GGCTCTGATGATGCAAAAGC | |||||
| N.3 | 780 | FTT0001 | dnaA | T | D | gcgggcGCAGATCTATAAACTCTTTGAAAt |
| C | A | gcgggcagggcggcGCAGATCTATAAACTCTTTGAAAc | ||||
| C | AATTTATTAAAGATTATGTAAATTCTATTCGT | |||||
| M.2 | 84027 | FTT0080 | tpiA | G | D | gcgggcagggcggcTCAGCTTTTAGGCTACCACCg |
| A | A | gcgggcTCAGCTTTTAGGCTACCACCa | ||||
| C | CAGGAGTTGTGGCTTCACTAGAGC | |||||
| A.2 | 1199395 | FTT1182c | vacJ | A | D | gcgggcGCATCAACACTATCACTAATCCCCTa |
| C | A | gcgggcagggcggcGCATCAACACTATCACTAATCCCCTc | ||||
| C | ATCACCAAGATTTTGCTGTGACATT | |||||
| A.3 | 62997 | FTT0062 | atpA | C | D | gcgggcagggcggcTGCTGTAGCTGCAACAATAATTGc |
| T | A | gcgggcTGCTGTAGCTGCAACAATAATTGt | ||||
| C | ATTGCAAACATTGTAAGACAGCTTGAAG | |||||
| A.4 | 830716 | FTT0810 | ybaB | T | D | gcgggcTCGGTAAGTATCGACAATTt |
| C | A | gcgggcagggcggcTCGGTAAGTATCGACAATTc | ||||
| C | AGCAGCTGCTATCAAATCTTC | |||||
| A.5 | 350750 | FTT0351 | rplQ | C | D | gcgggcagggcggcTAGAGGCTCAACGATTGc |
| T | A | gcgggcTAGAGGCTCAACGATTGt | ||||
| C | TGTCAGCTTCTTTGATTAATC | |||||
| A.6 | 1806912 | FTT1721 | purF | T | D | gcgggcTCGTACTCTTTAAAACCAAGCAt |
| C | A | gcgggcagggcggcTCGTACTCTTTAAAACCAAGCAc | ||||
| C | CTGAGGCTGTTTATAAAGCATGTAAAT | |||||
| B.15 | 1113816 | FTT1103 | G | D | gcgggcagggcggcTCAACTTGGAATCCAAGGCg | |
| A | A | gcgggcTCAACTTGGAATCCAAGGCa | ||||
| C | GCTTTGTTGATAGCTGCTTGGATACC | |||||
| B.16 | 608246 | FTT0588 | aroA | T | D | gcgggcATGCTAGCAAATTACCATCAAAAGt |
| G | A | gcgggcagggcggcATGCTAGCAAATTACCATCAAAAGg | ||||
| C | AACTCTTCTCGCCATCAACTTCTAT | |||||
| B.17 | 1743251 | FTT1673 | ribA | T | D | gcgggcCCAAGAGCTAAATTAGCTTCAAt |
| G | A | gcgggcagggcggcCCAAGAGCTAAATTAGCTTCAAg | ||||
| C | TGACCAAGAAGGTAGAGGTATTGGTT | |||||
| B.18 | 1756146 | FTT1686c | T | D | gcgggcAGCAGCAGGACAAATAGt | |
| C | A | gcgggcagggcggcAGCAGCAGGACAAATAGc | ||||
| C | TTGTGTCGATTCAAAACCAGACTTA | |||||
| B.19 | 1374034 | FTT1343c | A | D | gcgggcTTGCTACTGATGGTTTAACTa | |
| C | A | gcgggcagggcggcTTGCTACTGATGGTTTAACTc | ||||
| C | CAATACGTCACTTATGCAGTGAT | |||||
| B.20 | 1396117, | FTT1354, | pdpC | G | D | gcgggcagggcggcTCTGATGAAGAATATCTTACAg |
| 1789461 | FTT1709 | A | A | gcgggcTCTGATGAAGAATATCTTACAa | ||
| C | ATTATGGCAAAACTATACCTT | |||||
| B.21e | 701320 | FTT0684c | sthA | A | D | gcgggcACCAAGGTAGATTTGCAGCTACa |
| G | A | gcgggcagggcggcACCAAGGTAGATTTGCAGCTACg | ||||
| C | ATCCCTGTTGGGATATCCTCGACTAA | |||||
| B.22e | 1113320 | FTT1103 | A | D | gcgggcTGAATACTCTACGCGATAAGATa | |
| G | A | gcgggcagggcggcTGAATACTCTACGCGATAAGATg | ||||
| C | ATCAGACTTAGGTGTTAGATCAGAGTT | |||||
| B.23 | 253121 | FTT0240 | T | D | gcgggcTTACTACAAATTCGCCTCTAAt | |
| G | A | gcgggcagggcggcTTACTACAAATTCGCCTCTAAg | ||||
| C | AGCAAAAGAGCTTACTAAACAATTTGA | |||||
| B.24 | 1419996 | FTT1373 | fabH | G | D | gcgggcagggcggcTATCGCCAGGTTTAATTTGATg |
| T | A | gcgggcTATCGCCAGGTTTAATTTGATt | ||||
| C | TCTGCAGCATCTATCCCATTAGCCTTA | |||||
| B.25 | 1534495 | FTT1484c | aceF | T | D | gcgggcTGTATCTAAGACAGCAGTGAAGt |
| C | A | gcgggcagggcggcTGTATCTAAGACAGCAGTGAAGc | ||||
| C | ATGGTAGCATAGTTCTAGGAATAAACT |
a
GenBank accession no. AJ749949.
b
D, Primer with derived SNP state; A, Primer with ancestral SNP state; C, Common primer.
c
Primer tails and 3′-end mismatch base are in lower case.
d
No sequences with a G found by BLAST search against the nt database 2009/22/04, among isolates of the family of Francisellacae, uncultured and environmental Francisella-like bacteria.
e
B.21 is identical to Ft-SNP1 and B.22 is identical to Ft-SNP2 in Svensson et al 2009 (submitted manuscript).